taxonomy module of mmseqs2 v16 accepts only --search-type 3

[jasmezz]

When executing the MMSeqs2 taxonomy module on nucleotide contigs, I noticed a change between versions 15 and 16 of MMseqs2: While I always used the parameter --search-type with value 2 (= translated sequences), these runs (without changing anything than the version from 15 to 16) fail now with a segfault error in the blastp.sh script:

  tmp1/16844758798936012027/tmp_hsp1/8003483337503689507/blastp.sh: line 144:  1172 Segmentation fault      (core dumped) $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMP_PATH/pref_$STEP" $PREFILTER_PAR -s "$SENS"
  Error: Prefilter died
  Error: Search step died
  Error: First search died

When I run the same thing with --search-type 3 (i.e. nucleotide), it runs through successfully. None of the other values are being accepted.
I doubt that it fails because of too little memory because I reprocude the error even on really small input files, e.g. 5 short contigs or less.

Note that I always do fresh runs; i.e. the tmp1 folder is not recycled.

Do you have any insight on where this behaviour could come from? I would love to go back to --search-type 2 asap :)

[milot-mirdita]

This crash should be fixed in the newest release, at least I couldn't get it to crash on a small sample set earlier today.

[jasmezz]

Thanks! I can confirm it's fixed in version 17 👍

Although the same error (segfault of blastp.sh script) happens now for --search-type 3, but maybe that's a different issue.

[milot-mirdita]

Oh no :D What command did you run?

[jasmezz]

This one (worked so far with all previous versions that we used):

mmseqs \
      taxonomy \
      $DB_QUERY_PATH_NAME \
      $DB_TARGET_PATH_NAME \
      sample_1_taxonomy/sample_1 \
      tmp1 \
      --remove-tmp-files --search-type 3 --lca-ranks kingdom,phylum,class,order,family,genus,species --tax-lineage 1 -s 5.0 --orf-filter-s 2.0 --lca-mode 3 --vote-mode 1 --compressed 0 \
      --threads 4

Can assume that the two variables lead to the correct db paths ($DB_QUERY_PATH_NAME and $DB_QUERY_PATH_NAME I mean) :)